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Harper M, Nudurupati U, Workman RJ, Lakoba TI, Perez N, Nelson D, Ou Y, Punihaole D. Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy. J Chem Phys 2023; 159:225101. [PMID: 38078532 PMCID: PMC10720587 DOI: 10.1063/5.0177437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
We present structural models for three different amyloid fibril polymorphs prepared from amylin20-29 (sequence SNNFGAILSS) and amyloid-β25-35 (Aβ25-35) (sequence GSNKGAIIGLM) peptides. These models are based on the amide C=O bond and Ramachandran ψ-dihedral angle data from Raman spectroscopy, which were used as structural constraints to guide molecular dynamics (MD) simulations. The resulting structural models indicate that the basic structural motif of amylin20-29 and Aβ25-35 fibrils is extended β-strands. Our data indicate that amylin20-29 forms both antiparallel and parallel β-sheet fibril polymorphs, while Aβ25-35 forms a parallel β-sheet fibril structure. Overall, our work lays the foundation for using Raman spectroscopy in conjunction with MD simulations to determine detailed molecular-level structural models of amyloid fibrils in a manner that complements gold-standard techniques, such as solid-state nuclear magnetic resonance and cryogenic electron microscopy.
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Affiliation(s)
- Madeline Harper
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Uma Nudurupati
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Riley J. Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Taras I. Lakoba
- Department of Mathematics and Statistics, University of Vermont, Burlington, Vermont 05405, USA
| | - Nicholas Perez
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Delaney Nelson
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Yangguang Ou
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - David Punihaole
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
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Van Bruggen C, Punihaole D, Keith AR, Schmitz AJ, Tolar J, Frontiera RR, Reineke TM. Quinine copolymer reporters promote efficient intracellular DNA delivery and illuminate a protein-induced unpackaging mechanism. Proc Natl Acad Sci U S A 2020; 117:32919-32928. [PMID: 33318196 PMCID: PMC7777095 DOI: 10.1073/pnas.2016860117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Polymeric vehicles that efficiently package and controllably release nucleic acids enable the development of safer and more efficacious strategies in genetic and polynucleotide therapies. Developing delivery platforms that endogenously monitor the molecular interactions, which facilitate binding and release of nucleic acids in cells, would aid in the rational design of more effective vectors for clinical applications. Here, we report the facile synthesis of a copolymer containing quinine and 2-hydroxyethyl acrylate that effectively compacts plasmid DNA (pDNA) through electrostatic binding and intercalation. This polymer system poly(quinine-co-HEA) packages pDNA and shows exceptional cellular internalization, transgene expression, and low cytotoxicity compared to commercial controls for several human cell lines, including HeLa, HEK 293T, K562, and keratinocytes (N/TERTs). Using quinine as an endogenous reporter for pDNA intercalation, Raman imaging revealed that proteins inside cells facilitate the unpackaging of polymer-DNA complexes (polyplexes) and the release of their cargo. Our work showcases the ability of this quinine copolymer reporter to not only facilitate effective gene delivery but also enable diagnostic monitoring of polymer-pDNA binding interactions on the molecular scale via Raman imaging. The use of Raman chemical imaging in the field of gene delivery yields unprecedented insight into the unpackaging behavior of polyplexes in cells and provides a methodology to assess and design more efficient delivery vehicles for gene-based therapies.
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Affiliation(s)
- Craig Van Bruggen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - David Punihaole
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - Allison R Keith
- Department of Pediatrics, Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Andrew J Schmitz
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - Jakub Tolar
- Department of Pediatrics, Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455;
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455;
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Jakubek RS, Workman RJ, White SE, Asher SA. Polyglutamine Solution-State Structural Propensity Is Repeat Length Dependent. J Phys Chem B 2019; 123:4193-4203. [PMID: 31008597 DOI: 10.1021/acs.jpcb.9b01433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Expanded polyglutamine (polyQ) tracts in proteins, which are known to induce their aggregation, are associated with numerous neurodegenerative diseases. Longer polyQ tracts correlate with faster protein aggregation kinetics and a decreased age of onset for polyQ disease symptoms. Here, we use UV resonance Raman spectroscopy, circular dichroism spectroscopy, and metadynamics simulations to investigate the solution-state structures of the D2Q15K2 (Q15) and D2Q20K2 (Q20) peptides. Using metadynamics, we explore the conformational energy landscapes of Q15 and Q20 and investigate the relative energies and activation barriers between these low-energy structures. We compare the solution-state structures of D2Q10K2 (Q10), Q15, and Q20 to determine the dependence of polyQ structure on the Q tract length. We show that these peptides can adopt two distinct monomeric conformations: an aggregation-resistant PPII-like conformation and an aggregation-prone β-strand-like conformation. We find that longer polyQ peptides have an increased preference for the aggregation-prone β-strand-like conformation. This preference may play an important role in the increased aggregation rate of longer polyQ peptides that is thought to lead to decreased neurodegenerative disease age of onset for polyQ disease patients.
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Affiliation(s)
| | - Riley J Workman
- Department of Chemistry and Biochemistry, Center for Computational Sciences , Duquesne University , Pittsburgh , Pennsylvania 15282 , United States
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Jakubek RS, White SE, Asher SA. UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide. J Phys Chem B 2019; 123:1749-1763. [PMID: 30717595 DOI: 10.1021/acs.jpcb.8b10783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fibrillization of polyglutamine (polyQ) tracts in proteins is implicated in at least 10 neurodegenerative diseases. This generates great interest in the structure and the aggregation mechanism(s) of polyQ peptides. The fibrillization of polyQ is thought to result from the peptide's insolubility in aqueous solutions; longer polyQ tracts show decreased aqueous solution solubility, which is thought to lead to faster fibrillization kinetics. However, few studies have characterized the structure(s) of polyQ peptides with low solubility. In the work here, we use UV resonance Raman spectroscopy to examine the secondary structures, backbone hydrogen bonding, and side chain hydrogen bonding for a variety of solution-state, solid, and fibril forms of D2Q20K2 (Q20). Q20 is insoluble in water and has a β-strand-like conformation with extensive inter- and intrapeptide hydrogen bonding in both dry and aqueous environments. We find that Q20 has weaker backbone-backbone and backbone-side chain hydrogen bonding and is less ordered compared to that of polyQ fibrils. Interestingly, we find that the insoluble Q20 will form fibrils when incubated in water at room temperature for ∼5 h. Also, Q20 can be prepared using a well-known disaggregation procedure to produce a water-soluble PPII-like conformation with negligible inter- and intrapeptide hydrogen bonding and a resistance to aggregation.
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Punihaole D, Jakubek RS, Workman RJ, Asher SA. Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils. J Phys Chem Lett 2018; 9:1944-1950. [PMID: 29570305 DOI: 10.1021/acs.jpclett.8b00348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We determined an empirical correlation that relates the amide I vibrational band frequencies of the glutamine (Q) side chain to the strength of hydrogen bonding, van der Waals, and Lewis acid-base interactions of its primary amide carbonyl. We used this correlation to determine the Q side chain carbonyl interaction enthalpy (Δ Hint) in monomeric and amyloid-like fibril conformations of D2Q10K2 (Q10). We independently verified these Δ Hint values through molecular dynamics simulations that showed excellent agreement with experiments. We found that side chain-side chain and side chain-peptide backbone interactions in fibrils and monomers are more enthalpically favorable than are Q side chain-water interactions. Q10 fibrils also showed a more favorable Δ Hint for side chain-side chain interactions compared to backbone-backbone interactions. This work experimentally demonstrates that interamide side chain interactions are important in the formation and stabilization of polyQ fibrils.
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Affiliation(s)
- David Punihaole
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Ryan S Jakubek
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Riley J Workman
- Department of Chemistry and Biochemistry , Center for Computational Sciences, Duquesne University , Pittsburgh , Pennsylvania 15282 , United States
| | - Sanford A Asher
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
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Abstract
UV resonance Raman (UVRR) spectroscopy is a powerful tool for investigating the structure of biological molecules, such as proteins. Numerous UVRR spectroscopic markers that provide information on the structure and environment of the protein backbone and of amino acid side chains have recently been discovered. Combining these UVRR markers with hydrogen-deuterium exchange and advanced statistics is a powerful tool for studying protein systems, including the structure and formation mechanism of protein aggregates and amyloid fibrils. These techniques allow crucial new insights into the structure and dynamics of proteins, such as polyglutamine peptides, which are associated with 10 different neurodegenerative diseases. Here we summarize the spectroscopic structural markers recently developed and the important insights they provide.
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Punihaole D, Jakubek RS, Workman RJ, Marbella LE, Campbell P, Madura JD, Asher SA. Monomeric Polyglutamine Structures That Evolve into Fibrils. J Phys Chem B 2017; 121:5953-5967. [DOI: 10.1021/acs.jpcb.7b04060] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- David Punihaole
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ryan S. Jakubek
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Riley J. Workman
- Department
of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Lauren E. Marbella
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Patricia Campbell
- Department
of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Jeffry D. Madura
- Department
of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Sanford A. Asher
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Punihaole D, Workman RJ, Hong Z, Madura JD, Asher SA. Polyglutamine Fibrils: New Insights into Antiparallel β-Sheet Conformational Preference and Side Chain Structure. J Phys Chem B 2016; 120:3012-26. [PMID: 26947327 DOI: 10.1021/acs.jpcb.5b11380] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the structure of polyglutamine (polyQ) amyloid-like fibril aggregates is crucial to gaining insights into the etiology of at least ten neurodegenerative disorders, including Huntington's disease. Here, we determine the structure of D2Q10K2 (Q10) fibrils using ultraviolet resonance Raman (UVRR) spectroscopy and molecular dynamics (MD). Using UVRR, we determine the fibril peptide backbone Ψ and glutamine (Gln) side chain χ3 dihedral angles. We find that most of the fibril peptide bonds adopt antiparallel β-sheet conformations; however, a small population of peptide bonds exist in parallel β-sheet structures. Using MD, we simulate three different potential fibril structural models that consist of either β-strands or β-hairpins. Comparing the experimentally measured Ψ and χ3 angle distributions to those obtained from the MD simulated models, we conclude that the basic structural motif of Q10 fibrils is an extended β-strand structure. Importantly, we determine from our MD simulations that Q10 fibril antiparallel β-sheets are thermodynamically more stable than parallel β-sheets. This accounts for why polyQ fibrils preferentially adopt antiparallel β-sheet conformations instead of in-register parallel β-sheets like most amyloidogenic peptides. In addition, we directly determine, for the first time, the structures of Gln side chains. Our structural data give new insights into the role that the Gln side chains play in the stabilization of polyQ fibrils. Finally, our work demonstrates the synergistic power and utility of combining UVRR measurements and MD modeling to determine the structure of amyloid-like fibrils.
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Affiliation(s)
- David Punihaole
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Riley J Workman
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University , Pittsburgh, Pennsylvania 15282, United States
| | - Zhenmin Hong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Jeffry D Madura
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University , Pittsburgh, Pennsylvania 15282, United States
| | - Sanford A Asher
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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